A major veterans organization and an AIDS-research group have been left stranded by the investigation into the City Council’s phantom accounts, The Post has learned.

In a cruel bit of timing, paperwork allowing the Incarcerated Veterans Consortium on 125th Street to access nearly $200,000 was in the pipeline just as city Comptroller William Thompson put a freeze on all accounts tied to “member items” distributed by the council.

Edward Daniels, the consortium chairman, was baffled by the turn of events.

“It’s going to impact us in a very serious and negative way,” said Daniels, whose tiny organization opened in 1990.

Daniels said he couldn’t understand how his group got caught in the council slush-funds mess when it signed a contract with La Guardia Community College, which was acting as the conduit for the funds, last Dec. 17, 2007. He was told repeatedly that the money would be coming, most recently in March.

Also snared in the fiscal no-man’s land is the AIDS Community Research Initiative of America, which began an HIV-prevention program for older adults with seven community groups.

Executive Director Daniel Tietz said the group advanced $650,000 of its own money while awaiting a $1 million council grant, and can’t hold out much longer.

“I’m all for oversight and more accountability, but for heaven’s sake, do we have to throw out the baby with the bath water?” he said.

Thompson’s freeze took effect the week of April 13, 10 days after The Post revealed that millions of dollars in council funds were reserved in the names of fictitious groups so the money could be handed out to legitimate groups after the budget was adopted.

Officials confirmed that the incarcerated-veterans group, which also serves immigrant vets, became one of the scores of unintended victims of the council investigations.

“That’s one of the negatives of this whole situation,” said Councilman Hiram Monserrate (D-Queens), who secured the $1 million grant. “A lot of worthy groups are having their capacities to deliver services hampered.”